/*   asl_functions.cc various functions for the manipulation of ASL data

      Michael Chappell - FMIRB Image Analysis Group

      Copyright (C) 2009 University of Oxford */

/*  Part of FSL - FMRIB's Software Library
    http://www.fmrib.ox.ac.uk/fsl
    fsl@fmrib.ox.ac.uk
    
    Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
    Imaging of the Brain), Department of Clinical Neurology, Oxford
    University, Oxford, UK
    
    
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#include "asl_functions.h"

namespace OXASL {

  void data2stdform(Matrix& datamtx, vector<Matrix>& asldata, int ntis, bool isblocked, bool ispairs) {
    int nvox=datamtx.Ncols();
    int nmeas=datamtx.Nrows()/ntis;
    int nrpts;
    if (ispairs) nrpts=nmeas/2;
    else nrpts=nmeas;

    //cout << nmeas << " " << nrpts << " " << endl;

    if (isblocked)
      {
	Matrix thisti(nmeas,nvox);
	for (int ti=1; ti<=ntis; ti++) 
	  {
	    thisti=0;
	    //asldata[ti-1].ReSize(nvox,nmeas);
	    //extract the measurements for this TI
	    for (int i=1; i<=nrpts; i++)
	      {
		if (ispairs) {
		  thisti.Row(2*i-1) = datamtx.Row(2*(i-1)*ntis+2*ti-1);
		  thisti.Row(2*i) = datamtx.Row(2*(i-1)*ntis+2*ti);
		}
		else {
		  thisti.Row(i) = datamtx.Row((i-1)*ntis+ti);
		}
	      }
	  
	    asldata.push_back(thisti);
	  }

	/*
	//deal with orphan data at end (if present)
	if (datamtx.Nrows() > nmeas*ntis) {
	  int i=nrpts*2*ntis+1;
	  int ti=0;
	  while (i<= datamtx.Nrows()) {
	    if (ispairs) {
	      asldata[ti] = asldata[ti] & datamtx.Row(i);
	      i++;
	      if (i > datamtx.Nrows()) throw Exception("Cannot process this dataset as pairs: odd number of spare measurements at end");
	      asldata[ti] = asldata[ti] & datamtx.Row(i);
	    }
	    else {
	      asldata[ti] = asldata[ti] & datamtx.Row(i);
	    }
	    i++;
	    ti++;
	  }
	}
	*/
	
      }
    else 
      {

	for (int ti=1; ti<=ntis; ti++) 
	  //asldata[ti-1].ReSize(nvox,nmeas);
	  asldata.push_back(datamtx.Rows((ti-1)*nmeas+1,ti*nmeas));

	if (datamtx.Nrows() > nmeas*ntis) throw Exception("Orphaned data found at end of file - this is not logical when data is in TI blocks");
      }
  }

  void stdform2data(vector<Matrix>& asldata, Matrix& datareturn, bool outblocked, bool outpairs) {
    int ntis = asldata.size();
    int nvox = asldata[0].Ncols();
    int nmeas = asldata.back().Nrows(); //safer to determine this from the very last TI (in case of orphan measurements when nodiscard is turned on)
    int ninc=1;
    if (outpairs) ninc=2;
    
    if (outblocked) {
      datareturn.ReSize(ntis*nmeas,nvox);
      int idx=1;
      for (int m=1; m<=nmeas; m+=ninc)
	for (int ti=1; ti<=ntis; ti++) {
	  datareturn.Row(idx) = asldata[ti-1].Row(m);
	  idx++;
	  if (outpairs) {
	    datareturn.Row(idx) = asldata[ti-1].Row(m+1);
	    idx++;
	  }
	}
      assert(idx-1==ntis*nmeas);

      /*
      //deal with orphans
      if (asldata.front().Nrows() > nmeas) {
	int ti=0;
	int finalm = nmeas+ninc;
	while (asldata[ti].Nrows() > nmeas) {
	  datareturn.Row(idx) = asldata[ti].Row(finalm);
	  idx++;
	  if (outpairs) {
	    datareturn.Row(idx) = asldata[ti].Row(finalm+1);
	    idx++;
	  }
	  ti++;
	}
      }
      */
    }
    else {
      datareturn = asldata[0];
      for (int ti=1; ti<ntis; ti++) {
	datareturn &= asldata[ti];
      }
    }
  }

  void separatepairs(vector<Matrix>& asldata, vector<Matrix>& asldataodd, vector<Matrix>& asldataeven) {
    int ntis = asldata.size();
    int nmeas = asldata[0].Nrows();
    int nrpts=nmeas/2; //if we are using this function then the data must contain pairs

    // just in case the vectors are not empty to start with
    asldataodd.clear();
    asldataeven.clear();

    int idx;

    for (int ti=0; ti<ntis; ti++) {

	Matrix oddmtx;
	oddmtx = asldata[ti].Row(1);
	Matrix evenmtx;
	evenmtx = asldata[ti].Row(2);

	for (int r=2; r<=nrpts; r++) {
	  idx=(r-1)*2+1;
	  oddmtx &= asldata[ti].Row(idx);
	  evenmtx &= asldata[ti].Row(idx+1);
	}
	asldataodd.push_back(oddmtx);
	asldataeven.push_back(evenmtx);
      }
  }

  void mergepairs(vector<Matrix>& asldata, vector<Matrix>& asldataodd, vector<Matrix>&asldataeven) {
    int ntis = asldataodd.size();
    int nmeas = asldataodd[0].Nrows();
    int nrpts=nmeas; //asldataodd does not contain pairs

    asldata.clear(); //make sure this is clear

    for (int ti=0; ti<ntis; ti++) {
      Matrix aslmtx;
      aslmtx = asldataodd[ti].Row(1);
      aslmtx &= asldataeven[ti].Row(1);
      for (int r=2; r<=nrpts; r++) {
	aslmtx &= asldataodd[ti].Row(r);
	aslmtx &= asldataeven[ti].Row(r);
      }
      asldata.push_back(aslmtx);
    }
  }

  void timeans(vector<Matrix>& asldata, vector<Matrix>& meanreturn) {
    int ntis = asldata.size();
    int nvox = asldata[0].Ncols();
    Matrix meanti(ntis,nvox);
      for (int n=0; n<ntis; n++) 
	{
	  meanreturn.push_back(mean(asldata[n],1));
	}
  }

  void timeanout(vector<Matrix>& asldata, volume<float>& mask, string fname, bool outpairs) {
      cout << "Outputting ASL data mean at each TI" << endl;
      
	vector<Matrix> meanti;
      if (!outpairs) {
	timeans(asldata,meanti);
      }
      else {
	//need to preserve pairs in the data - separate
	vector<Matrix> asldataodd;
	vector<Matrix> asldataeven;
	separatepairs(asldata,asldataodd,asldataeven);

	//take mean of odds and evens
	vector<Matrix> meanodd;
	timeans(asldataodd,meanodd);
	vector<Matrix> meaneven;
	timeans(asldataeven,meaneven);

	//recombine
	mergepairs(meanti,meanodd,meaneven);
      }

      Matrix meantimat;
      stdform2data(meanti, meantimat, false, false);

      volume4D<float> meanout;
      meanout.setmatrix(meantimat,mask);
      save_volume4D(meanout,fname);
      
    }

  void splitout(vector<Matrix>& asldata, volume<float>& mask, string froot) {
      cout << "Splitting ASL data into files for each TI" << endl;
      int ntis = asldata.size();
      volume4D<float> blockout;
      for (int n=0; n<ntis; n++) 
	{
	  char cstr [5];
	  if (n<10) sprintf(cstr,"00%d",n);
	  else if (n<100) sprintf(cstr,"0%d",n);
	  else if (n<1000) sprintf(cstr,"%d",n);
	  else throw Exception("More than 1000 measurements in this ASL data file, sorry cannot handle this operation");
	  string tino(cstr);
	  
	  blockout.setmatrix(asldata[n],mask);
	  save_volume4D(blockout,froot+tino);
	}
    }

  void genepochs(vector<Matrix>& asldata, vector<Matrix>& epochreturn, int eplen, int epol) {
      
      int ntis = asldata.size();
      int nvox = asldata[0].Ncols();
      int nmeas = asldata[0].Nrows();

      epochreturn.clear();

      if (epol>=eplen) throw Exception("The epoch overlap may not exceed or equal the length of the epoch");
      int epadv = eplen-epol;

      int e=1;
      Matrix epoch_temp(ntis,nvox);
      while ((e-1)*epadv+eplen<=nmeas)
	{
	  //Matrix ti_temp(eplen,nvox);
	  //go through the TIs
	  for (int ti=1; ti<=ntis; ti++) {
	    epoch_temp.Row(ti) = mean(asldata[ti-1].Rows((e-1)*epadv+1,(e-1)*epadv+eplen),1);
	  }

	  epochreturn.push_back(epoch_temp);

	  e++;
	}

      e--; //correct for final e++
      int unused=nmeas-( (e-1)*epadv+eplen );
      if (unused>0) cout << "Number of measurements from end of data discarded: " << unused << endl;
    }

  void gentiepochs(Matrix& asldata, vector<Matrix>& epochreturn, int eplen, int epol) {
      // expects data in matrix form (blocks of repeats)

      int nvox = asldata.Ncols();
      int nmeas = asldata.Nrows();

      epochreturn.clear();

      if (epol>=eplen) throw Exception("The epoch overlap may not exceed or equal the length of the epoch");
      int epadv = eplen-epol;

      int e=1;
      Matrix epoch_temp(eplen,nvox);
      while ((e-1)*epadv+eplen<=nmeas)
	{
	  epoch_temp = asldata.Rows( (e-1)*epadv+1,(e-1)*epadv+eplen );
	  epochreturn.push_back(epoch_temp);
	  e++;
	}

      e--;
      
      int unused=nmeas-( (e-1)*epadv+eplen );
      if (unused>0) cout << "Number of measurements from end of data discarded: " << unused << endl;
    }


    void epochout(vector<Matrix>& asldata, volume<float>& mask, string froot, int eplen, int epol, bool outpairs, bool tiunit) {
      //Save out epochs of data.
      // tiunit indicates that we want epochs to be done over the Tis rather than over the repeats
    cout << "Ouput ASL data epochs" << endl;
 
    //generate the epochs
    vector<Matrix> theepochs;
    Matrix alldata;
    if (!outpairs) {
      if (!tiunit) {
	genepochs(asldata, theepochs, eplen, epol);
      }
      else {
	// epochs over the TIs need to convert the data to matrix form
	stdform2data(asldata,alldata,true,false);
	gentiepochs(alldata,theepochs,eplen,epol);
      }
    }
    else {
      //need to preserve pairs in the data - separate
      vector<Matrix> asldataodd;
      vector<Matrix> asldataeven;
      separatepairs(asldata,asldataodd,asldataeven);

      vector<Matrix> oddepochs;
      if (!tiunit) {
	genepochs(asldataodd, oddepochs, eplen, epol);
      }
      else {
	stdform2data(asldataodd,alldata,true,false);
	gentiepochs(alldata, oddepochs, eplen, epol);
      }

      vector<Matrix> evenepochs;
      if (!tiunit) {
	genepochs(asldataeven, evenepochs, eplen, epol);
      }
      else {
	stdform2data(asldataodd,alldata,true,false);
	gentiepochs(alldata, evenepochs, eplen, epol);
	
      }

      mergepairs(theepochs,oddepochs,evenepochs);
    }

    int nepoch = theepochs.size();
    volume4D<float> epochout;
    for (int e=0; e<nepoch; e++) {
      char cstr [5];
	  if (e<10) sprintf(cstr,"00%d",e);
	  else if (e<100) sprintf(cstr,"0%d",e);
	  else if (e<1000) sprintf(cstr,"%d",e);
	  else throw Exception("More than 1000 epochs in this ASL data file, sorry cannot handle this operation");
	  string epno(cstr);

	  epochout.setmatrix(theepochs[e],mask);
	  save_volume4D(epochout,froot+epno);
    }
  }

  ReturnMatrix SVDdeconv(const Matrix& data, const Matrix& aif) {
    // do a singular value deconvolution of the data to get residue function

    int nti = data.Nrows();
    int nvox = data.Ncols();
    float truncfac = 0.2;

    // voxelwise SVD deconvolution
    Matrix aifconv; Matrix residue(nti,nvox);
    DiagonalMatrix S; DiagonalMatrix D; Matrix U; Matrix V;
    for (int v=1; v<=nvox; v++) {
      //make convolution matrix
      aifconv = convmtx(aif.Column(v));
      //SVD
      SVD(aifconv,S,U,V);
      // invert the singular values
      D = S.i();
      // truncate (zero all singular values below threshold)
      for (int i=2; i<=D.Nrows(); i++) {
	if (S(i,i) < truncfac*S(1,1)) D(i,i)=0;
      }
      // calculate resdiue
      residue.Column(v) = V*D*U.t()*data.Column(v);
    }
      
    return residue; 
  }

  ReturnMatrix convmtx(const ColumnVector& invec){
    // create a (simple) convolution matrix

    int nentry = invec.Nrows();
    Matrix cmat(nentry,nentry);
    cmat=0.0;
    for (int i=1; i<=nentry; i++) {
      cmat.SubMatrix(i,i,1,i) = ((invec.Rows(1,i)).Reverse()).AsRow();
    }

    return cmat;
  }

  void deconvout(vector<Matrix>& asldata, volume<float>& mask, Matrix& aif, string fname) {
    //perform deconvolution and output the magnitude and residue function

    //take the mean in each TI (we dont want mulitple repeats here)
    vector<Matrix> meandata;
    timeans(asldata, meandata);
    Matrix data;
    stdform2data(meandata,data,false,false); //way to get mean result from standard form into a matrix that can now be processed

    //do the deconvolution
    Matrix resid = SVDdeconv(data,aif);
    // extract magntiude and residue separately
    int nvox = data.Ncols();
    ColumnVector mag(nvox);
    for (int v=1; v<=nvox; v++) {
      mag(v) = (resid.Column(v)).Maximum();
      resid.Column(v) /= mag(v);
    }

    //output 
    volume4D<float> residout;
    residout.setmatrix(resid,mask);
    save_volume4D(residout,fname+"_residuals");

    volume4D<float> magout;
    magout.setmatrix(mag.AsMatrix(1,nvox),mask);
    save_volume4D(magout,fname+"_magntiude");
  }



}